1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Alam, S.L. Sun, J. Payne, M. Welch, B.D. Blake, B.K. Davis, D.R. Meyer, H.H. Emr, S.D. Sundquist, W.I. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic C3 H7 N O2 89.093 y ALANINE L-peptide linking C6 H15 N4 O2 1 175.209 y ARGININE L-peptide linking C4 H8 N2 O3 132.118 y ASPARAGINE L-peptide linking C4 H7 N O4 133.103 y ASPARTIC ACID L-peptide linking C3 H7 N O2 S 121.158 y CYSTEINE L-peptide linking C5 H10 N2 O3 146.144 y GLUTAMINE L-peptide linking C5 H9 N O4 147.129 y GLUTAMIC ACID L-peptide linking C2 H5 N O2 75.067 y GLYCINE peptide linking C6 H10 N3 O2 1 156.162 y HISTIDINE L-peptide linking C6 H13 N O2 131.173 y ISOLEUCINE L-peptide linking C6 H13 N O2 131.173 y LEUCINE L-peptide linking C6 H15 N2 O2 1 147.195 y LYSINE L-peptide linking C5 H11 N O2 S 149.211 y METHIONINE L-peptide linking C9 H11 N O2 165.189 y PHENYLALANINE L-peptide linking C5 H9 N O2 115.130 y PROLINE L-peptide linking C3 H7 N O3 105.093 y SERINE L-peptide linking C4 H9 N O3 119.119 y THREONINE L-peptide linking C11 H12 N2 O2 204.225 y TRYPTOPHAN L-peptide linking C9 H11 N O3 181.189 y TYROSINE L-peptide linking C5 H11 N O2 117.146 y VALINE L-peptide linking Zn 2 65.409 ZINC ION non-polymer UK Embo J. EMJODG 0897 0261-4189 23 1411 1421 10.1038/sj.emboj.7600114 15029239 Ubiquitin interactions of NZF zinc fingers. 2004 US J.Biol.Chem. JBCHA3 0071 0021-9258 278 20225 20234 10.1074/jbc.M300459200 Structure and ubiquitin interactions of the conserved zinc finger domain of Npl4. 2003 10.2210/pdb1q5w/pdb pdb_00001q5w 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 1 SINGLE WAVELENGTH M 1 1.0 3376.865 homolog of yeast nuclear protein localization 4 Npl4 NZF domain (residues 580-608) 1 man polymer 8576.831 Ubiquitin 1 man polymer 65.409 ZINC ION 1 syn non-polymer no no GSTSAMWACQHCTFMNQPGTGHCEMCSLPRT GSTSAMWACQHCTFMNQPGTGHCEMCSLPRT A polypeptide(L) no no MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG B polypeptide(L) n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n Norway rat Rattus Escherichia Escherichia coli sample NPL4 10116 Rattus norvegicus 469008 Escherichia coli BL21(DE3) BL21(DE3) T7 pGEX2T human Homo Escherichia Escherichia coli sample (UBA52 OR UBCEP2) AND UBB AND UBC AND (UBA80 OR UBCEP1 OR RPS27A) 9606 Homo sapiens 469008 Escherichia coli BL21(DE3) BL21(DE3) T7 pET3d database_2 pdbx_nmr_software pdbx_struct_assembly pdbx_struct_conn_angle pdbx_struct_oper_list struct_conn struct_ref_seq_dif struct_site repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations 1 0 2004-03-30 1 1 2008-04-29 1 2 2011-07-13 1 3 2022-03-02 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_nmr_software.name _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.value _struct_conn.pdbx_dist_value _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_ref_seq_dif.details _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id Npl4 Zinc finger structure RCSB Y RCSB 2003-08-11 REL ZN ZINC ION inter-molecular NOEs identified with half-filtered and double half-filtered NOE experiments and samples #1 and #2. structures with the least restraint violations,structures with the lowest energy,target function 200 20 3D_13C-separated_NOESY 3D_15N-separated_NOESY HNCACB, CBCACONH, CCONH, HCCONH,HNCO, HNCACO 3D_13C-separated_NOESY 3D_15N-separated_NOESY HNCACB, CBCACONH, CCONH, HCCONH,HNCO, HNCACO 70mM 5.5 ambient 291 K 70mM 5.5 ambient 291 K 70mM 5.5 ambient 291 K 70mM 5.5 ambient 291 K structures are based on 2072 NOE-derived distance constraints, 145 dihedral angle constraints ,104 H-Bond constraints, and 14 Zinc-coordination constraints. Torsion angle dynamics followed by simulated annealing 1 fewest violations,lowest energy 1mM Npl4 NZF U-15N,13C; 2mM unlabeled-Ubiquitin; 20mM phosphate buffer pH 5.5, 50mM NaCl; 90% H2O, 10% 90% H2O/10% D2O 1mM Ubiquitin U-15N,13C; 2mM unlabeled-Npl4 NZF; 20mM phosphate buffer pH 5.5, 50mM NaCl; 90% H2O, 10% 90% H2O/10% D2O 1mM Ubiquitin U-15N; 2mM unlabeled-Npl4 NZF; 20mM phosphate buffer pH 5.5, 50mM 90% H2O/10% D2O 1mM Npl4 NZF U-15N; 2mM unlabeled-Ubiquitin; 20mM phosphate buffer pH 5.5, 50mM NaCl; 90% H2O, 10% 90% H2O/10% D2O Peter Guntert refinement DYANA 1.5 "CRYSTALLOGRAPHY AND NMR SYSTEM (CNS): A NEW SOFTWARE SYSTEM refinement CNS 1.1 www.accelrys.com processing Felix 97 T.D. Goddard and D.G. Kneller, SPARKY 3, data analysis Sparky 3.106 600 Varian INOVA ZN2 32 3 ZN ZN 32 A GLY 1 n 1 GLY 1 A SER 2 n 2 SER 2 A THR 3 n 3 THR 3 A SER 4 n 4 SER 4 A ALA 5 n 5 ALA 5 A MET 6 n 6 MET 6 A TRP 7 n 7 TRP 7 A ALA 8 n 8 ALA 8 A CYS 9 n 9 CYS 9 A GLN 10 n 10 GLN 10 A HIS 11 n 11 HIS 11 A CYS 12 n 12 CYS 12 A THR 13 n 13 THR 13 A PHE 14 n 14 PHE 14 A MET 15 n 15 MET 15 A ASN 16 n 16 ASN 16 A GLN 17 n 17 GLN 17 A PRO 18 n 18 PRO 18 A GLY 19 n 19 GLY 19 A THR 20 n 20 THR 20 A GLY 21 n 21 GLY 21 A HIS 22 n 22 HIS 22 A CYS 23 n 23 CYS 23 A GLU 24 n 24 GLU 24 A MET 25 n 25 MET 25 A CYS 26 n 26 CYS 26 A SER 27 n 27 SER 27 A LEU 28 n 28 LEU 28 A PRO 29 n 29 PRO 29 A ARG 30 n 30 ARG 30 A THR 31 n 31 THR 31 A MET 101 n 1 MET 101 B GLN 102 n 2 GLN 102 B ILE 103 n 3 ILE 103 B PHE 104 n 4 PHE 104 B VAL 105 n 5 VAL 105 B LYS 106 n 6 LYS 106 B THR 107 n 7 THR 107 B LEU 108 n 8 LEU 108 B THR 109 n 9 THR 109 B GLY 110 n 10 GLY 110 B LYS 111 n 11 LYS 111 B THR 112 n 12 THR 112 B ILE 113 n 13 ILE 113 B THR 114 n 14 THR 114 B LEU 115 n 15 LEU 115 B GLU 116 n 16 GLU 116 B VAL 117 n 17 VAL 117 B GLU 118 n 18 GLU 118 B PRO 119 n 19 PRO 119 B SER 120 n 20 SER 120 B ASP 121 n 21 ASP 121 B THR 122 n 22 THR 122 B ILE 123 n 23 ILE 123 B GLU 124 n 24 GLU 124 B ASN 125 n 25 ASN 125 B VAL 126 n 26 VAL 126 B LYS 127 n 27 LYS 127 B ALA 128 n 28 ALA 128 B LYS 129 n 29 LYS 129 B ILE 130 n 30 ILE 130 B GLN 131 n 31 GLN 131 B ASP 132 n 32 ASP 132 B LYS 133 n 33 LYS 133 B GLU 134 n 34 GLU 134 B GLY 135 n 35 GLY 135 B ILE 136 n 36 ILE 136 B PRO 137 n 37 PRO 137 B PRO 138 n 38 PRO 138 B ASP 139 n 39 ASP 139 B GLN 140 n 40 GLN 140 B GLN 141 n 41 GLN 141 B ARG 142 n 42 ARG 142 B LEU 143 n 43 LEU 143 B ILE 144 n 44 ILE 144 B PHE 145 n 45 PHE 145 B ALA 146 n 46 ALA 146 B GLY 147 n 47 GLY 147 B LYS 148 n 48 LYS 148 B GLN 149 n 49 GLN 149 B LEU 150 n 50 LEU 150 B GLU 151 n 51 GLU 151 B ASP 152 n 52 ASP 152 B GLY 153 n 53 GLY 153 B ARG 154 n 54 ARG 154 B THR 155 n 55 THR 155 B LEU 156 n 56 LEU 156 B SER 157 n 57 SER 157 B ASP 158 n 58 ASP 158 B TYR 159 n 59 TYR 159 B ASN 160 n 60 ASN 160 B ILE 161 n 61 ILE 161 B GLN 162 n 62 GLN 162 B LYS 163 n 63 LYS 163 B GLU 164 n 64 GLU 164 B SER 165 n 65 SER 165 B THR 166 n 66 THR 166 B LEU 167 n 67 LEU 167 B HIS 168 n 68 HIS 168 B LEU 169 n 69 LEU 169 B VAL 170 n 70 VAL 170 B LEU 171 n 71 LEU 171 B ARG 172 n 72 ARG 172 B LEU 173 n 73 LEU 173 B ARG 174 n 74 ARG 174 B GLY 175 n 75 GLY 175 B GLY 176 n 76 GLY 176 B author_defined_assembly 2 dimeric A CYS 9 A SG CYS 9 1_555 A ZN 32 C ZN ZN 1_555 A CYS 12 A SG CYS 12 1_555 107.4 A CYS 9 A SG CYS 9 1_555 A ZN 32 C ZN ZN 1_555 A CYS 23 A SG CYS 23 1_555 104.2 A CYS 12 A SG CYS 12 1_555 A ZN 32 C ZN ZN 1_555 A CYS 23 A SG CYS 23 1_555 113.0 A CYS 9 A SG CYS 9 1_555 A ZN 32 C ZN ZN 1_555 A CYS 26 A SG CYS 26 1_555 103.7 A CYS 12 A SG CYS 12 1_555 A ZN 32 C ZN ZN 1_555 A CYS 26 A SG CYS 26 1_555 124.8 A CYS 23 A SG CYS 23 1_555 A ZN 32 C ZN ZN 1_555 A CYS 26 A SG CYS 26 1_555 101.7 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 x,y,z identity operation 0.0000000000 0.0000000000 0.0000000000 A N TRP 7 A N TRP 7 A O ASN 16 A O ASN 16 B O ILE 113 B O ILE 13 B N VAL 105 B N VAL 5 B N PHE 104 B N PHE 4 B O LEU 167 B O LEU 67 B O HIS 168 B O HIS 68 B N ILE 144 B N ILE 44 4 A A H O CYS LEU 23 28 1.59 7 A A H O CYS LEU 23 28 1.59 7 A A H O CYS PHE 9 14 1.59 9 A A H O CYS LEU 23 28 1.59 10 A A H O CYS PHE 9 14 1.58 12 A A H O CYS LEU 23 28 1.57 14 A A H O CYS LEU 23 28 1.58 18 B B H O VAL ILE 105 113 1.58 1 A SER 4 -65.56 -170.19 1 A CYS 9 -46.57 157.59 1 A HIS 11 -131.99 -57.86 1 A THR 13 81.06 23.53 1 B ASP 121 -63.98 -167.62 1 B ASN 160 86.63 44.04 2 A SER 2 -176.64 144.16 2 A THR 3 -98.90 31.60 2 A ALA 5 -177.63 122.90 2 A CYS 9 -47.57 157.21 2 A HIS 11 -132.31 -57.81 2 B ASP 121 -61.92 -165.12 2 B ASN 160 85.74 51.46 2 B SER 165 -59.00 173.30 2 B ARG 174 46.24 -169.16 3 A THR 3 -176.71 102.41 3 A ALA 5 62.07 -176.23 3 A CYS 9 -46.79 157.45 3 A HIS 11 -137.81 -54.11 3 A THR 13 54.77 74.19 3 B ASP 121 -65.29 -168.07 3 B ALA 146 39.13 41.69 3 B ASN 160 83.89 50.47 4 A SER 2 -176.42 -40.43 4 A ALA 5 -92.62 50.85 4 A CYS 9 -48.64 157.41 4 A HIS 11 -130.73 -57.37 4 A MET 25 -123.02 -58.92 4 B ASP 121 -64.37 -167.66 4 B ASN 160 84.29 49.72 5 A SER 2 60.83 102.56 5 A SER 4 -127.99 -74.81 5 A ALA 5 -166.36 50.30 5 A CYS 9 -47.78 157.45 5 A HIS 11 -135.25 -55.89 5 A MET 25 -123.04 -59.65 5 B ASP 121 -58.09 -165.60 5 B ASN 160 86.59 50.62 5 B SER 165 -58.58 171.96 6 A SER 2 -161.90 106.58 6 A THR 3 60.36 155.62 6 A CYS 9 -47.22 157.19 6 A HIS 11 -137.53 -56.80 6 B ASP 121 -60.31 -165.28 6 B ASN 160 86.77 50.17 7 A SER 2 61.62 113.79 7 A THR 3 -163.75 -69.36 7 A ALA 5 -176.82 124.54 7 A CYS 9 -46.40 157.41 7 A HIS 11 -130.21 -54.36 7 B ASP 121 -58.98 -165.80 7 B ASN 160 83.26 48.79 7 B SER 165 -59.19 172.98 7 B ARG 174 -59.59 172.99 8 A SER 2 -60.38 -176.22 8 A THR 3 -99.00 31.76 8 A CYS 9 -48.21 156.81 8 A HIS 11 -135.88 -56.44 8 A MET 25 -123.13 -60.67 8 B ASP 121 -60.26 -166.61 8 B ASN 160 87.42 48.35 8 B LEU 173 -68.14 -173.94 9 A SER 2 -176.72 -40.33 9 A ALA 5 -92.08 50.50 9 A CYS 9 -48.23 157.54 9 A HIS 11 -128.03 -57.60 9 B ASP 121 -60.68 -165.77 9 B ASN 160 82.91 52.44 10 A THR 3 -171.86 100.01 10 A ALA 5 75.84 48.82 10 A CYS 9 -48.05 157.83 10 A HIS 11 -131.19 -54.55 10 A MET 25 -123.13 -59.47 10 B ASP 121 -60.49 -164.91 10 B ASN 160 83.18 49.24 10 B ARG 174 59.32 165.63 11 A THR 3 -172.44 129.84 11 A SER 4 -130.36 -68.39 11 A ALA 5 -160.50 52.05 11 A CYS 9 -46.84 157.51 11 A HIS 11 -135.05 -53.49 11 A THR 13 54.50 74.45 11 A MET 25 -123.09 -61.00 11 B ASP 121 -59.51 -167.90 11 B ALA 146 39.39 41.33 11 B ASN 160 83.48 52.86 12 A SER 2 68.00 -71.24 12 A THR 3 60.30 79.93 12 A SER 4 -98.05 -67.26 12 A ALA 5 61.00 -176.22 12 A CYS 9 -42.92 157.00 12 A HIS 11 -135.35 -53.75 12 A THR 13 53.42 74.19 12 A MET 25 -120.24 -59.97 12 B ASP 121 -60.47 -165.21 12 B ASN 160 83.21 54.04 13 A CYS 9 -46.21 157.17 13 A HIS 11 -138.85 -52.77 13 A MET 25 -123.03 -61.62 13 B ASP 121 -58.11 -165.93 13 B ASN 160 81.89 56.52 14 A CYS 9 -46.71 157.11 14 A HIS 11 -133.60 -53.17 14 A THR 13 56.13 73.32 14 A MET 25 -123.11 -61.01 14 A SER 27 80.23 14.91 14 B ASP 121 -59.77 -165.60 14 B ASN 160 84.11 51.85 15 A SER 2 60.50 -178.92 15 A CYS 9 -47.19 157.47 15 B ASP 121 -57.84 -169.39 15 B ASN 160 83.33 54.43 15 B SER 165 -58.34 172.28 16 A SER 2 60.19 158.64 16 A SER 4 60.10 -171.13 16 A CYS 9 -47.92 157.42 16 A THR 13 53.73 76.39 16 A MET 25 -122.40 -60.31 16 B ASP 121 -60.60 -167.63 16 B ALA 146 39.24 41.22 16 B ASN 160 85.27 50.37 17 A SER 2 -131.68 -68.14 17 A THR 3 61.57 114.10 17 A SER 4 60.82 -172.77 17 A CYS 9 -47.46 156.81 17 A THR 13 53.45 77.07 17 A MET 25 -123.05 -60.84 17 B ASP 121 -59.20 -167.52 17 B ALA 146 38.37 41.30 17 B ASN 160 85.71 51.56 17 B SER 165 -57.81 172.95 18 A SER 4 60.23 83.29 18 A CYS 9 -46.61 157.33 18 A HIS 11 -137.28 -55.36 18 A THR 13 51.11 73.06 18 A MET 25 -122.98 -61.80 18 B ASP 121 -61.09 -167.84 18 B ALA 146 37.78 41.25 18 B ASN 160 82.08 53.75 19 A CYS 9 -45.71 156.78 19 A HIS 11 -144.49 -55.30 19 A MET 25 -123.13 -59.12 19 B ASP 121 -59.69 -167.11 19 B ALA 146 36.70 43.49 19 B ASN 160 88.43 47.58 20 A SER 2 -173.37 36.29 20 A SER 4 -60.40 -170.09 20 A ALA 5 -94.49 50.78 20 A CYS 9 -46.43 157.54 20 A HIS 11 -137.82 -56.30 20 A MET 25 -120.19 -59.11 20 B ASP 121 -60.33 -166.09 20 B ASN 160 85.43 50.49 20 B SER 165 -56.11 172.03 Ubiquitin Recognition by Npl4 Zinc-Fingers 1 N N 2 N N 3 N N B THR 122 B THR 22 HELX_P B GLU 134 B GLU 34 1 1 13 metalc 2.376 A CYS 9 A SG CYS 9 1_555 A ZN 32 C ZN ZN 1_555 metalc 2.318 A CYS 12 A SG CYS 12 1_555 A ZN 32 C ZN ZN 1_555 metalc 2.411 A CYS 23 A SG CYS 23 1_555 A ZN 32 C ZN ZN 1_555 metalc 2.379 A CYS 26 A SG CYS 26 1_555 A ZN 32 C ZN ZN 1_555 PROTEIN BINDING Ubiquitin, Protein-Protein complex, Zinc-finger, Rubredoxin knuckle, NZF domain, PROTEIN BINDING NPL4_RAT UNP 1 580 Q9ES54 TSAMWACQHCTFMNQPGTGHCEMCSLPRT UBIQ_HUMAN UNP 2 1 P62988 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG 580 608 1Q5W 3 31 Q9ES54 A 1 3 31 1 76 1Q5W 101 176 P62988 B 2 1 76 1 cloning artifact GLY 1 1Q5W A Q9ES54 UNP 1 1 cloning artifact SER 2 1Q5W A Q9ES54 UNP 2 2 4 anti-parallel anti-parallel parallel anti-parallel A TRP 7 A TRP 7 A ALA 8 A ALA 8 A MET 15 A MET 15 A ASN 16 A ASN 16 B THR 112 B THR 12 B GLU 116 B GLU 16 B GLN 102 B GLN 2 B THR 107 B THR 7 B SER 165 B SER 65 B LEU 171 B LEU 71 B GLN 141 B GLN 41 B ILE 144 B ILE 44 BINDING SITE FOR RESIDUE ZN A 32 A ZN 32 Software 4 A CYS 9 A CYS 9 4 1_555 A CYS 12 A CYS 12 4 1_555 A CYS 23 A CYS 23 4 1_555 A CYS 26 A CYS 26 4 1_555